1TRO | pdb_00001tro

CRYSTAL STRUCTURE OF TRP REPRESSOR OPERATOR COMPLEX AT ATOMIC RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb1TRO/pdb
• NAKB: 1TRO

• Classification: TRANSCRIPTION/DNA
• Organism(s): Escherichia coli str. K-12 substr. W3110
• Mutation(s): No 


• Deposited: 1992-08-30 Released: 1994-01-31 
• Deposition Author(s): Otwinowski, Z., Schevitz, R.W., Zhang, R.-G., Lawson, C.L., Joachimiak, A., Marmorstein, R., Luisi, B.F., Sigler, P.B.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Observed: 
  0.167 (Depositor) 

Literature

Crystal structure of trp repressor/operator complex at atomic resolution.

Otwinowski, Z., Schevitz, R.W., Zhang, R.G., Lawson, C.L., Joachimiak, A., Marmorstein, R.Q., Luisi, B.F., Sigler, P.B.

(1988) Nature 335: 321-329

• PubMed: 3419502 
• DOI: https://doi.org/10.1038/335321a0
• Primary Citation Related Structures: 
  1TRO


• PubMed Abstract: 
  

  The crystal structure of the trp repressor/operator complex shows an extensive contact surface, including 24 direct and 6 solvent-mediated hydrogen bonds to the phosphate groups of the DNA. There are no direct hydrogen bonds or non-polar contacts to the bases that can explain the repressor's specificity for the operator sequence. Rather, the sequence seems to be recognized indirectly through its effects on the geometry of the phosphate backbone, which in turn permits the formation of a stable interface. Water-mediated polar contacts to the bases also appear to contribute part of the specificity.

---

Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, University of Chicago, Illinois 60637.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 73.58 kDa 
• Atom Count: 5,373 
• Modeled Residue Count: 477 
• Deposited Residue Count: 508 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (TRP REPRESSOR)	E [auth A], F [auth C], G [auth E], H [auth G]	108	Escherichia coli str. K-12 substr. W3110	Mutation(s): 0
UniProt
Find proteins for P0A881 (Escherichia coli (strain K12)) Explore P0A881  Go to UniProtKB:  P0A881

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*GP*TP*AP*CP*TP*AP*GP*TP*TP*AP*AP*CP*TP*AP*GP*T P*AP*C)-3')	A [auth I], B [auth J], C [auth K], D [auth L]	19	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRP	I [auth A], J [auth A], K [auth E], L [auth G]	TRYPTOPHAN C11 H12 N2 O2 QIVBCDIJIAJPQS-VIFPVBQESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.65	α = 90
b = 72.43	β = 94.96
c = 107.39	γ = 90

Software Package:

Software Name	Purpose
PROLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-01-31 
Deposition Author(s): Otwinowski, Z., Schevitz, R.W., Zhang, R.-G., Lawson, C.L., Joachimiak, A., Marmorstein, R., Luisi, B.F., Sigler, P.B.

Revision History  

• Version 1.0: 1994-01-31
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2020-05-13
  Changes: Data collection, Database references, Structure summary
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations